open-source tools for PRoxY System Modeling, v1.0: oxygen-isotope systems

The paper, published in JAMES: http://onlinelibrary.wiley.com/doi/10.1002/2015MS000447/full

Proxy system modeling can be used in paleoclimatology to improve the interpretation of paleoclimate data. Existing forward models for climate proxies are somewhat scattered in the literature, making their integration difficult. Further, each model has been coded separately, according to disparate conventions. Here, we present a comprehensive, consistently formatted package of forward models for water-isotope based climate proxies (ice cores, corals, tree ring cellulose, and speleothem calcite) [PRYSM]. This suite of Python-scripted models requires a standard set of climate inputs and can be used to simulate the proxy variable of interest by proxy class. By making this forward modeling toolbox publicly available, PRYSM provides an accessible platform that maximizes the utility of proxy data and facilitates proxy-climate (simulated or historical) comparisons. Many of these codes have been employed in past studies; we review modeling approaches for each proxy class, and compare results when forced with an isotope-enabled climate simulation. Applications of multi-proxy forward modeling including parameter estimation, the effects of physical processes (such as karst transit times or firn diffusion in ice cores) on the simulated climate signal, as well as explicit modeling of time uncertainties are used to demonstrate the utility of PRYSM for a broad array of climate studies.

python 2.7 (https://www.python.org/download/releases/2.7/)

numpy (http://www.numpy.org/)
scipy (http://www.scipy.org/)
rpy2 (http://rpy.sourceforge.net/) (For BCHRON)

Optional: matplotlib (http://matplotlib.org/) (For plotting tools)

Make sure the dependencies are installed, then download and unzip this package, and then:
python setup.py install

Alternately, you can use pip:
pip install git+https://github.com/sylvia-dee/PRYSM.git

Either method will add a module named 'psm' to your default lib/python2.7/site-packages/ directory.

If you lack root access:
python setup.py install --user

For git users: git clone https://github.com/sylvia-dee/PRYSM.git python setup.py install

From the examples/ directory, run each of the example driver scripts and each of the plotting examples. For just the icecore example:
python icecore_driver.py

This will create numpy array output files in examples/results/:
ice_Xn.npy ice_time_d.npy ice_depth.npy ice_diffused.npy

To plot (requires matplotlib):
python plot_icecore_example.py

This will reproduce paper figure 3.